This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The MMTSB web pages (http://mmtsb.scripps.edu) are maintained to provide web services to the scientific community, distribute and support software tools developed within the resource, offer general information about the MMTSB resource and its projects, and provide selected links to related resources. Already available web services include the very successful and established Virus Particle Explorer Database (VIPERdb) as well as some utility functions for nucleic acid and protein modeling applications, in particular for interconversion between reduced lattice models and all-atom representation and the Go-model server. The MMTSB web site itself is the distribution site for the MMTSB Tool Set that is being developed for multiscale protein modeling and structure prediction application. It is a collection of modules, mostly written in perl to ensure portability and allow for easy modifications and extensions. This tool set provides interfaces to CHARMM, Amber, MONSSTER, PSIRED and MODELLER specifically geared towards protein and nucleic acid modeling applications and implements new methods developed within the resources for model interconversion and advanced sampling techniques. The design of the tool set is highly modular offering easy-to-use application-oriented utilities as well as flexible programming interfaces for more complex customized applications.